Question about lacking of two python packages

[FeiGao0717]

Hello, I met a question when I use the quantify_transcript_flames. This is my code:

quantify_transcript_flames(
annotation = annotation,
outdir = outdir,
config = jsonlite::fromJSON(system.file('extdata/config_sclr_nanopore_3end.json', package = 'FLAMES')),
pipeline = "sc_single_sample"
)

And there is an error because of lacking of the two packages: pysam=0.21.0 cutadapt=4.4

I use anaconda to activate a new environment and install the two packages but the problem can't be solved. It seems that the envrionment is set up by the basilisk and the two packages can't be install from conda.anaconda.org.

09:28:46 Sun Sep 29 2024 quantify transcripts 
Found realignment file(s):  realign2transcript.bam
+ /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/bin/conda create --yes --prefix /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/FLAMES/1.11.1/flames_env 'python=3.10' --quiet -c conda-forge -c bioconda -c defaults
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/FLAMES/1.11.1/flames_env

  added / updated specs:
    - python=3.10

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.1-hc14010f_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h7bae524_1
  openssl            conda-forge/osx-arm64::openssl-3.3.2-h8359307_0
  pip                conda-forge/noarch::pip-24.2-pyh8b19718_1
  python             conda-forge/osx-arm64::python-3.10.15-h7d35d02_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  tzdata             conda-forge/noarch::tzdata-2024a-h8827d51_1
  wheel              conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/bin/conda install --yes --prefix /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/FLAMES/1.11.1/flames_env 'python=3.10' -c conda-forge -c bioconda -c defaults
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.7.1

Please update conda by running

    $ conda update -n base -c defaults conda

# All requested packages already installed.

+ /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/bin/conda install --yes --prefix /Users/gaofei/Library/Caches/org.R-project.R/R/basilisk/1.16.0/FLAMES/1.11.1/flames_env -c conda-forge -c bioconda -c defaults 'python=3.10' 'python=3.10' 'numpy=1.25.0' 'scipy=1.11.1' 'pysam=0.21.0' 'cutadapt=4.4' 'tqdm=4.64.1' 'pandas=1.3.5' 'oarfish=0.6.2'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pysam=0.21.0
  - cutadapt=4.4

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Error: one or more Python packages failed to install [error code 1]

[FeiGao0717]

Hi @SagarChandra07 ! Firstly, thanks for your help! The package seems like a windows exe document, but my system is mac. I wonder if there is a package for mac system or other way to solve this problem. Thank you very much!

[ChangqingW]

This is fixed with the newest commit on Github, you can install it with BiocManager::install("mritchielab/FLAMES"), you might also want to install the latest basilisk and basiliskl.util via devtools::install_github('Bioconductor/basilisk.utils') and devtools::install_github('Bioconductor/basilisk').

[ChangqingW]

Hi @SagarChandra07 ! Firstly, thanks for your help! The package seems like a windows exe document, but my system is mac. I wonder if there is a package for mac system or other way to solve this problem. Thank you very much!

That is probably malware, the user has already been reported and deleted.